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cov-lineages / pango-designation

Repository for suggesting new lineages that should be added to the current scheme
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Suggestion to broaden XDV.1.2 to include everything under S:R346T branch. #2789

Open xz-keg opened 1 month ago

xz-keg commented 1 month ago

The only XDV.1+S:R346T seqs were the N:I292T branch when XDV.1.2 was designated. However as more seqs are submitted there are many more branches now. Suggest to broaden XDV.1.2 accordingly. @AngieHinrichs @corneliusroemer

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice2_genome_test_5dd41_689d60.json?label=id:node_5496004 image

FedeGueli commented 1 month ago

The only XDV.1+S:R346T seqs were the N:I292T branch when XDV.1.2 was designated. However there are many more branches now. Suggest to broaden XDV.1.2 accordingly. @AngieHinrichs @corneliusroemer

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice2_genome_test_5dd41_689d60.json?label=id:node_5496004 image

They doesnt seem related if not the orf1a:L3116F carrying ones.

FedeGueli commented 1 month ago

Or you think they are all related being mostly by Shanxi?

xz-keg commented 1 month ago

They doesnt seem related if not the orf1a:L3116F carrying ones.

Like JN.1.16.1, they shall be assigned a name despite potential separate occurence.

FedeGueli commented 1 month ago

They doesnt seem related if not the orf1a:L3116F carrying ones.

Like JN.1.16.1, they shall be assigned a name despite potential separate occurence.

Yeah but already assigned, it is very rare that a lineage has been broadened or tightened, classical example AY.41 that was designated too deep leavig out a lineage, sibling of AY.103, that was deadly in eastern Europe during summer 2021.

xz-keg commented 1 month ago

They doesnt seem related if not the orf1a:L3116F carrying ones.

Like JN.1.16.1, they shall be assigned a name despite potential separate occurence.

Yeah but already assigned, it is very rare that a lineage has been broadened or tightened, classical example AY.41 that was designated too deep leavig out a lineage, sibling of AY.103, that was deadly in eastern Europe during summer 2021.

They do not have a name and is under the general XDV.1, while XDV.1.2 now starts from N:I292T

FedeGueli commented 1 month ago

They do not have a name and is under the general XDV.1, while XDV.1.2 now starts from N:I292T

i mean most of them are on XDV.1.2 with starting with 346T it would become the collector of XDV.1 +346T but likely already hard to think there will be new emergence of 346T directly from the politomy after many months around so likely worth broadening it.

DailyCovidCases commented 1 month ago

@xz-keg I think you can close this issue now